blah blah
This file belongs to the repository: https://github.com/drisso/awst_analysis.
The code is released with license GPL v3.0.
(Note: I don’t think we can release these images with GPL license, to be removed from final file) # Benchmarking single cell RNA-sequencing analysis pipelines using mixture control experiments (Nature) ### Supplementary Figure 3 Visualization of representative benchmarking datasets using t-SNE and UMAP and violin plot of the number of doublets. (a) t-SNE and UMAP visualizations of 4 datasets. From left to right: 10X single cell using 3 cell lines; 10X single cell using 5 cell lines; a CEL-seq2 cell mixture and a CEL-seq2 RNA mixture. Each point represents a cell or ‘pseudo cell’ and the number of cells in each plot is indicated in the title. (b) Violin plot of doublets in each dataset, identified using Demuxlet (DBL: doublet, SNG: single cell). The number of single cells and doublets are shown on top of each violin. Doublets were excluded when calculating the performance metrics.
awstif (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("drisso/awst")
#BiocManager::install("GIS-SP-Group/RCA")
#BiocManager::install("hgu133plus2.db")
library(awst)
library(EDASeq)
library(SingleCellExperiment)
jobName <- "mixoloy20200904"
source(url("https://raw.githubusercontent.com/drisso/awst_analysis/master/functions.R"))
true_number_of_clusters <- c(3, 5, 7, 10, 10)
names(true_number_of_clusters) <- c("sc_10x", "sc_10x_5cl", "RNAmix_celseq2", "cellmix4", "cellmix3")
####
results <- matrix(NA, ncol = 5, nrow = 21)
colnames(results) <- c("where", "what", "silhouette", "NDE", "R2")
k <- 1
save_plots <- FALSE
compute_r2 <- function(y, labs) {
if(all(y==0)) {
return(NA)
}
fit <- lm(y ~ labs)
res <- summary(fit)
return(res$r.squared)
}
get_r2 <- function(datamat, labs) {
r2 <- apply(datamat, 2, compute_r2, labs)
return(r2)
}
compute_de <- function(y, labs) {
if(all(y==0)) {
return(1)
}
fit <- lm(y ~ labs)
res <- anova(fit)
return(res[1,5])
}
get_de <- function(datamat, labs) {
pvals <- apply(datamat, 2, compute_de, labs)
pvals <- sort(pvals)
return(datamat[,names(pvals)[1:500]])
}
prefix <- "sc_10x_5cl"
con <- gzcon(url("https://github.com/LuyiTian/sc_mixology/blob/master/data/csv/sc_10x_5cl.metadata.csv.gz?raw=true"))
annotation.df <- read.csv(textConnection(readLines(con)))
annotation.df$cell.col <- factor(annotation.df$cell_line)
levels(annotation.df$cell.col) <- c("gold", "red", "blue", "magenta", "green3")
annotation.df$cell.col <- as.character(annotation.df$cell.col)
annotation.df$cell_line <- paste0("mix", annotation.df$mix)
con <- gzcon(url("https://github.com/LuyiTian/sc_mixology/blob/master/data/csv/sc_10x_5cl.count.csv.gz?raw=true"))
ddata <- read.csv(textConnection(readLines(con)))
both <- intersect(colnames(ddata), rownames(annotation.df))
ddata <- ddata[, both]
annotation.df <- annotation.df[both,]
prefix <- "sc_10x_5cl"
save(ddata, annotation.df, prefix, file = paste0(prefix, "_counts.RData"))
library(awst)
library(EDASeq)
library(SingleCellExperiment)
load(paste0(prefix, "_counts.RData"))
no_of_detected_gene_per_sample <- colSums(ddata > 0)
fivenum(no_of_detected_gene_per_sample)
ddata <- EDASeq::betweenLaneNormalization(as.matrix(ddata), which = "full", round = FALSE)
# apply the AWS-transformation
tmp <- rowSums(ddata)
sum(tmp > 0)
tmp <- colSums(ddata)
sum(tmp > 0)
exprData <- awst(ddata, poscount = TRUE, full_quantile = TRUE)
sum(is.na(rowSums(exprData)))
sum(is.na(colSums(exprData)))
save(exprData, prefix, file = paste0(prefix, "_expression.RData"))
nrow_exprData <- nrow(exprData)
ncol_exprData <- ncol(exprData)
# library(irlba)
# pprcomp <- prcomp_irlba(exprData, 5) # Run PC analysis
#
# set.seed(2020)
# ans_Rtsne <- Rtsne(exprData, pca = FALSE) # Run TSNE
#
# set.seed(2020)
# ans_umap <- umap(exprData) # Run Umap
#
# save(nrow_exprData, ncol_exprData, annotation.df,
# pprcomp, ans_Rtsne, ans_umap, prefix,
# file = paste0(prefix, "_expression_working.RData"))
save(nrow_exprData, ncol_exprData, annotation.df, prefix,
file = paste0(prefix, "_expression_working.RData"))
load(paste0(prefix, "_counts.RData"))
load(paste0(prefix, "_expression.RData"))
# get random subset (to be removed)
set.seed(135)
cellidx <- sample(colnames(ddata), 100)
ddata <- ddata[,cellidx]
annotation.df <- annotation.df[cellidx,]
# awst (exprData)
system.time({
fq <- EDASeq::betweenLaneNormalization(as.matrix(ddata), which = "full", round = FALSE)
exprData <- awst(fq, poscount = TRUE, full_quantile = TRUE)
})
user system elapsed 0.223 0.020 0.242
exprData_gf <- awst::gene_filter(exprData, heterogeneity_threshold = .1)
dim(exprData_gf)
[1] 100 6068
# VST
library(DESeq2)
get_hvg <- function(mat, k=1000) {
vars <- matrixStats::rowVars(mat)
names(vars) <- rownames(mat)
vars <- sort(vars, decreasing = TRUE)
mat <- mat[names(vars)[seq_len(k)],]
return(mat)
}
dds <- DESeqDataSetFromMatrix(ddata, colData = annotation.df,
design = ~1)
# dds <- estimateSizeFactors(dds)
# dds <- estimateDispersions(dds)
system.time({
vst <- varianceStabilizingTransformation(dds, blind=FALSE)
vst <- assay(vst)
vst1000 <- get_hvg(vst, k=1000)
vst2500 <- get_hvg(vst, k=2500)
vst5000 <- get_hvg(vst, k=5000)
})
user system elapsed 10.348 6.587 7.013
system.time({
# rlog
rld <- rlog(dds, blind=FALSE)
rld <- assay(rld)
rld1000 <- get_hvg(rld, k=1000)
rld2500 <- get_hvg(rld, k=2500)
rld5000 <- get_hvg(rld, k=5000)
})
## rlog() may take a long time with 50 or more samples,
## vst() is a much faster transformation
user system elapsed
2694.783 4084.403 292.784
# Townes
library(scry)
library(SingleCellExperiment)
system.time({
sce <- SingleCellExperiment(assays = list(counts = ddata),
colData = annotation.df)
sce <- nullResiduals(sce, assay="counts", type="deviance")
sce <- nullResiduals(sce, assay="counts", type="pearson")
res_deviance <- assay(sce, "binomial_deviance_residuals")
# res_deviance <- get_hvg(res_deviance)
res_pearson <- assay(sce, "binomial_pearson_residuals")
# res_pearson <- get_hvg(res_deviance)
})
user system elapsed 2.339 4.259 0.346
# CPM
system.time({
cpm <- t(get_CPM(ddata))
cpm1000 <- get_hvg(cpm, k=1000)
cpm2500 <- get_hvg(cpm, k=2500)
cpm5000 <- get_hvg(cpm, k=5000)
})
user system elapsed 0.062 0.000 0.062
# raw
raw <- as.matrix(ddata)
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
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user system elapsed 0.335 0.008 0.343 [1] 100 15028 user system elapsed 13.720 9.499 9.487
## rlog() may take a long time with 50 or more samples,
## vst() is a much faster transformation
user system elapsed
3933.004 5974.970 429.755 user system elapsed 2.831 4.870 0.404 user system elapsed 0.088 0.000 0.087
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
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## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
user system elapsed 0.290 0.002 0.292 [1] 100 6228
## -- note: fitType='parametric', but the dispersion trend was not well captured by the
## function: y = a/x + b, and a local regression fit was automatically substituted.
## specify fitType='local' or 'mean' to avoid this message next time.
user system elapsed 21.951 24.092 10.322
## rlog() may take a long time with 50 or more samples,
## vst() is a much faster transformation
## -- note: fitType='parametric', but the dispersion trend was not well captured by the
## function: y = a/x + b, and a local regression fit was automatically substituted.
## specify fitType='local' or 'mean' to avoid this message next time.
user system elapsed
2789.856 4126.596 301.494 user system elapsed 2.683 4.702 0.368 user system elapsed 0.079 0.003 0.082
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
## Warning in anova.lm(fit): ANOVA F-tests on an essentially perfect fit are
## unreliable
sessionInfo()
## R version 4.0.0 (2020-04-24)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 18.04.4 LTS
##
## Matrix products: default
## BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=C
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] stats4 parallel stats graphics grDevices utils datasets
## [8] methods base
##
## other attached packages:
## [1] cluster_2.1.0 scry_1.0.1
## [3] DESeq2_1.28.1 SingleCellExperiment_1.10.1
## [5] EDASeq_2.22.0 ShortRead_1.46.0
## [7] GenomicAlignments_1.24.0 SummarizedExperiment_1.18.2
## [9] DelayedArray_0.14.1 matrixStats_0.56.0
## [11] Rsamtools_2.4.0 GenomicRanges_1.40.0
## [13] GenomeInfoDb_1.24.2 Biostrings_2.56.0
## [15] XVector_0.28.0 IRanges_2.22.2
## [17] S4Vectors_0.26.1 BiocParallel_1.22.0
## [19] Biobase_2.48.0 BiocGenerics_0.34.0
## [21] awst_0.0.4 knitr_1.28
## [23] BiocManager_1.30.10
##
## loaded via a namespace (and not attached):
## [1] bitops_1.0-6 bit64_0.9-7 RColorBrewer_1.1-2
## [4] progress_1.2.2 httr_1.4.1 tools_4.0.0
## [7] R6_2.4.1 colorspace_1.4-1 DBI_1.1.0
## [10] tidyselect_1.1.0 prettyunits_1.1.1 bit_1.1-15.2
## [13] curl_4.3 compiler_4.0.0 rtracklayer_1.48.0
## [16] scales_1.1.1 genefilter_1.70.0 askpass_1.1
## [19] rappdirs_0.3.1 DESeq_1.39.0 stringr_1.4.0
## [22] digest_0.6.25 rmarkdown_2.2 R.utils_2.9.2
## [25] jpeg_0.1-8.1 pkgconfig_2.0.3 htmltools_0.4.0
## [28] umap_0.2.5.0 dbplyr_1.4.4 rlang_0.4.6
## [31] RSQLite_2.2.0 generics_0.0.2 jsonlite_1.6.1
## [34] hwriter_1.3.2 dplyr_1.0.0 R.oo_1.23.0
## [37] RCurl_1.98-1.2 magrittr_1.5 GenomeInfoDbData_1.2.3
## [40] Matrix_1.2-18 munsell_0.5.0 Rcpp_1.0.4.6
## [43] reticulate_1.16 lifecycle_0.2.0 R.methodsS3_1.8.0
## [46] stringi_1.4.6 yaml_2.2.1 MASS_7.3-51.6
## [49] zlibbioc_1.34.0 BiocFileCache_1.12.1 grid_4.0.0
## [52] blob_1.2.1 crayon_1.3.4 lattice_0.20-41
## [55] splines_4.0.0 GenomicFeatures_1.40.1 annotate_1.66.0
## [58] hms_0.5.3 locfit_1.5-9.4 pillar_1.4.4
## [61] geneplotter_1.66.0 biomaRt_2.44.1 XML_3.99-0.3
## [64] glue_1.4.1 evaluate_0.14 latticeExtra_0.6-29
## [67] png_0.1-7 vctrs_0.3.1 gtable_0.3.0
## [70] openssl_1.4.1 purrr_0.3.4 assertthat_0.2.1
## [73] ggplot2_3.3.1 xfun_0.14 aroma.light_3.18.0
## [76] xtable_1.8-4 RSpectra_0.16-0 survival_3.1-12
## [79] glmpca_0.2.0 tibble_3.0.1 AnnotationDbi_1.50.3
## [82] memoise_1.1.0 ellipsis_0.3.1
| where | what | silhouette | NDE | R2 |
|---|---|---|---|---|
| raw | sc_10x_5cl | 0.0666 | 500 | 0.5448 |
| cpm | sc_10x_5cl | 0.0462 | 500 | 0.5693 |
| awst | sc_10x_5cl | 0.0990 | 500 | 0.5141 |
| vst | sc_10x_5cl | 0.0731 | 500 | 0.5983 |
| rlog | sc_10x_5cl | 0.1427 | 500 | 0.6014 |
| deviance | sc_10x_5cl | 0.1370 | 500 | 0.5906 |
| pearson | sc_10x_5cl | 0.1232 | 500 | 0.5546 |
| raw | sc_10x | 0.1194 | 500 | 0.6635 |
| cpm | sc_10x | 0.0734 | 500 | 0.6840 |
| awst | sc_10x | 0.1286 | 500 | 0.6588 |
| vst | sc_10x | 0.1207 | 500 | 0.6984 |
| rlog | sc_10x | 0.1567 | 500 | 0.7015 |
| deviance | sc_10x | 0.2050 | 500 | 0.6724 |
| pearson | sc_10x | 0.1677 | 500 | 0.6251 |
| raw | RNAmix_celseq2 | -0.0415 | 500 | 0.3194 |
| cpm | RNAmix_celseq2 | -0.0151 | 500 | 0.3718 |
| awst | RNAmix_celseq2 | -0.0083 | 500 | 0.3458 |
| vst | RNAmix_celseq2 | -0.0184 | 500 | 0.4259 |
| rlog | RNAmix_celseq2 | 0.0118 | 500 | 0.4378 |
| deviance | RNAmix_celseq2 | 0.0093 | 500 | 0.4376 |
| pearson | RNAmix_celseq2 | 0.0086 | 500 | 0.4343 |
knitr::knit_exit()